X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fschemes%2FPIDColourSchemeTest.java;h=c2f86d6e24b1602065e8770fdb9e73dac3e0e522;hb=61632514caf99d7897843f8bb3e4378aa715d040;hp=6f60e50245194d6a5cfa6708256ae04d1a7e64d7;hpb=9270bd30c65a1304c4228b2f07734bc8461cd531;p=jalview.git

diff --git a/test/jalview/schemes/PIDColourSchemeTest.java b/test/jalview/schemes/PIDColourSchemeTest.java
index 6f60e50..c2f86d6 100644
--- a/test/jalview/schemes/PIDColourSchemeTest.java
+++ b/test/jalview/schemes/PIDColourSchemeTest.java
@@ -4,9 +4,9 @@ import static org.testng.Assert.assertEquals;
 
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Color;
 
@@ -35,13 +35,14 @@ public class PIDColourSchemeTest
    * <li>case insensitive matching</li>
    * <ul>
    */
-  @Test
+  @Test(groups = "Functional")
   public void testFindColour()
   {
     ColourSchemeI scheme = new PIDColourScheme();
 
     /*
      * doesn't use column or sequence
+     * we assume consensus residue is computed as upper case
      */
     assertEquals(scheme.findColour('A', 0, null, "A", 0f), white);
     assertEquals(scheme.findColour('A', 0, null, "A", 40f), white);
@@ -54,8 +55,6 @@ public class PIDColourSchemeTest
     assertEquals(scheme.findColour('A', 0, null, "KFV", 100f), white);
 
     assertEquals(scheme.findColour('a', 0, null, "A", 80f), over60);
-    assertEquals(scheme.findColour('A', 0, null, "a", 80f), over60);
-    assertEquals(scheme.findColour('a', 0, null, "a", 80f), over60);
     assertEquals(scheme.findColour('A', 0, null, "AC", 80f), over60);
     assertEquals(scheme.findColour('A', 0, null, "KCA", 80f), over60);
   }
@@ -65,7 +64,7 @@ public class PIDColourSchemeTest
    * option on the annotation label popup menu) results in a change to the
    * colouring
    */
-  @Test
+  @Test(groups = "Functional")
   public void testFindColour_ignoreGaps()
   {
     /*
@@ -78,10 +77,26 @@ public class PIDColourSchemeTest
      * first column PID is 50%, or 67% ignoring gaps
      */
     String seqs = ">seq1\nAAAAA\n>seq2\nAAAAA\n>seq3\n-CCCC\n>seq4\nFFFFF\n";
+
+    /*
+     * load data and wait for consensus to be computed
+     */
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqs,
             DataSourceType.PASTE);
-    AlignViewport viewport = af.getViewport();
+    AlignmentViewport viewport = af.getViewport();
     viewport.setIgnoreGapsConsensus(false, af.alignPanel);
+    while (viewport.getConsensusSeq() == null)
+    {
+      synchronized (this)
+      {
+        try
+        {
+          wait(50);
+        } catch (InterruptedException e)
+        {
+        }
+      }
+    }
     af.changeColour_actionPerformed(JalviewColourScheme.PID.toString());
 
     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
@@ -90,7 +105,7 @@ public class PIDColourSchemeTest
      * including gaps, A should be coloured for 50% consensus
      */
     Color c = viewport
-            .getViewportColourScheme().findColour('A', 0, seq);
+            .getResidueShading().findColour('A', 0, seq);
     assertEquals(c, over40);
 
     /*
@@ -98,7 +113,7 @@ public class PIDColourSchemeTest
      */
     viewport.setIgnoreGapsConsensus(true, af.alignPanel);
     c = viewport
-            .getViewportColourScheme().findColour('A', 0, seq);
+            .getResidueShading().findColour('A', 0, seq);
     assertEquals(c, over60);
   }
 }